Sh3bp2

Overview
NameSh3bp2
Smed IDSMED30021695
Length (bp)1467
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 



 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)




Explore this single cell expression dataset with our NB Cluster Shiny App




 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of Sh3bp2 (SMED30021695) t-SNE clustered cells

Violin plots show distribution of expression levels for Sh3bp2 (SMED30021695) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of Sh3bp2 (SMED30021695) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Sh3bp2 (SMED30021695) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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Embryonic Expression

Davies et. al., 2017




Hover the mouse over a column in the graph to view average RPKM values per sample.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020




SMED30021695

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymal cellSMED30021695SMESG000054964.1 SMESG000072377.1 SMESG000072363.1 dd_Smed_v4_8268_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30021695SMESG000054964.1 SMESG000072377.1 SMESG000072363.1 dd_Smed_v4_8268_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Sh3bp2 vs. TrEMBL
Match: S5WMZ9 (Sh3bp2 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 73.9442 bits (180), Expect = 1.245e-10
Identity = 34/83 (40.96%), Postives = 52/83 (62.65%), Query Frame = 3
Query:   48 PAQELLKDPNVGFSRVLKHNFSKKNYLNRWVKCFIIITKGILYVYSSTESTKPYMIVLLGIFQEIEKVKNAMESPTWVFHLHP 296
            PAQ LL+ PN+ FS +L+ + + K  L++WVKC++I+ +G +Y+Y +  S  P    +L  F E   +KN  +SP WVF L P
Sbjct:    5 PAQSLLRKPNITFSGILETSKTSKMSLHKWVKCYVIVFEGNIYIYENCLSESPKSTNVLSKFNEFHVLKNRKKSPLWVFILQP 87          

HSP 2 Score: 62.3882 bits (150), Expect = 7.711e-7
Identity = 35/97 (36.08%), Postives = 55/97 (56.70%), Query Frame = 3
Query:  573 LKNIIFSGTSEAAYKELFHNFYLGSFLVRQNDDRQVLTVQSKDKVLKYVLNTNPETKLISVNKQKMEFDNLQCLLSYYQEFDLPWEKLKLTIPYKLV 863
            +++ IF+GT E A   L     +G +L+R   DRQVL+VQ++  ++KY L  NP T+ +S+     EF NL  L+ +Y   ++P    +L  PY  V
Sbjct:  220 MRDFIFNGTREEAAAVLSKVQQIGGYLIRVQGDRQVLSVQTERGIVKYKLYKNPLTERVSIQGFGNEFYNLTDLVKHYYTNNIPNYTCRLKCPYGSV 316          
BLAST of Sh3bp2 vs. Planmine SMEST
Match: SMESG000072377.1 (SMESG000072377.1)

HSP 1 Score: 280.796 bits (717), Expect = 5.127e-119
Identity = 140/155 (90.32%), Postives = 141/155 (90.97%), Query Frame = 3
Query:  417 AKQAMDFRNFTLTANNKGSSQRALFQIPPEGEVTLNSSIFGYYDFAYQNPLNLKNIIFSGTSEAAYKELFHNFYLGSFLVRQNDDRQVLTVQSKDKVLKYVLNTNPETKLISVNKQKMEFDNLQCLLSYYQEFDLPWEKLKLTIPYKLVDRDEWL 881
            +KQAMDFRNFTLTANNKGSSQRALFQIPPEGEVTLNSSIFGYYDFAYQNPLNLKNIIFSGTS              SFLVRQNDDRQVLTVQSKDKVLKYVLNTNPETKLISVNKQKMEFDNLQCLLSYYQEFDLPWEKLKLTIPYKLVDRDEWL
Sbjct:   78 SKQAMDFRNFTLTANNKGSSQRALFQIPPEGEVTLNSSIFGYYDFAYQNPLNLKNIIFSGTS--------------SFLVRQNDDRQVLTVQSKDKVLKYVLNTNPETKLISVNKQKMEFDNLQCLLSYYQEFDLPWEKLKLTIPYKLVDRDEWL 218          

HSP 2 Score: 167.548 bits (423), Expect = 5.127e-119
Identity = 77/79 (97.47%), Postives = 77/79 (97.47%), Query Frame = 2
Query:  134 MGEMFHYNYKRHSLCLFKYRIDKTIHDCFIGYISRNRESQECNGISNVGFPFTSTPRTTNYASVRFRNGSIIRCRHLCK 370
            MGEMFHYNYKRHSLCLFKYRIDKTIHDCFIGYISRNRESQECNGISNVGFPFTS PRTTNYASVRFRNGSIIRCRHL K
Sbjct:    1 MGEMFHYNYKRHSLCLFKYRIDKTIHDCFIGYISRNRESQECNGISNVGFPFTSAPRTTNYASVRFRNGSIIRCRHLSK 79          
BLAST of Sh3bp2 vs. Planmine SMEST
Match: SMESG000072377.1 (SMESG000072377.1)

HSP 1 Score: 280.411 bits (716), Expect = 7.845e-117
Identity = 140/155 (90.32%), Postives = 141/155 (90.97%), Query Frame = 3
Query:  417 AKQAMDFRNFTLTANNKGSSQRALFQIPPEGEVTLNSSIFGYYDFAYQNPLNLKNIIFSGTSEAAYKELFHNFYLGSFLVRQNDDRQVLTVQSKDKVLKYVLNTNPETKLISVNKQKMEFDNLQCLLSYYQEFDLPWEKLKLTIPYKLVDRDEWL 881
            +KQAMDFRNFTLTANNKGSSQRALFQIPPEGEVTLNSSIFGYYDFAYQNPLNLKNIIFSGTS              SFLVRQNDDRQVLTVQSKDKVLKYVLNTNPETKLISVNKQKMEFDNLQCLLSYYQEFDLPWEKLKLTIPYKLVDRDEWL
Sbjct:   75 SKQAMDFRNFTLTANNKGSSQRALFQIPPEGEVTLNSSIFGYYDFAYQNPLNLKNIIFSGTS--------------SFLVRQNDDRQVLTVQSKDKVLKYVLNTNPETKLISVNKQKMEFDNLQCLLSYYQEFDLPWEKLKLTIPYKLVDRDEWL 215          

HSP 2 Score: 160.229 bits (404), Expect = 7.845e-117
Identity = 74/76 (97.37%), Postives = 74/76 (97.37%), Query Frame = 2
Query:  143 MFHYNYKRHSLCLFKYRIDKTIHDCFIGYISRNRESQECNGISNVGFPFTSTPRTTNYASVRFRNGSIIRCRHLCK 370
            MFHYNYKRHSLCLFKYRIDKTIHDCFIGYISRNRESQECNGISNVGFPFTS PRTTNYASVRFRNGSIIRCRHL K
Sbjct:    1 MFHYNYKRHSLCLFKYRIDKTIHDCFIGYISRNRESQECNGISNVGFPFTSAPRTTNYASVRFRNGSIIRCRHLSK 76          
BLAST of Sh3bp2 vs. Planmine SMEST
Match: SMESG000072363.1 (SMESG000072363.1)

HSP 1 Score: 224.557 bits (571), Expect = 6.377e-72
Identity = 106/109 (97.25%), Postives = 107/109 (98.17%), Query Frame = 3
Query:   27 MTIERILPAQELLKDPNVGFSRVLKHNFSKKNYLNRWVKCFIIITKGILYVYSSTESTKPYMIVLLGIFQEIEKVKNAMESPTWVFHLHPHPELQTMPQLDFGTEVLSD 353
            MTI+RIL AQELLKDPNVGFSRVLKHNFSKKNYLNRWVKCFIIITKGILYVYSSTESTKPYMIVLLGIFQEIEKVKNAMESPTWVFHLHPHPELQTM QLDFGTEVLSD
Sbjct:    1 MTIDRILHAQELLKDPNVGFSRVLKHNFSKKNYLNRWVKCFIIITKGILYVYSSTESTKPYMIVLLGIFQEIEKVKNAMESPTWVFHLHPHPELQTMSQLDFGTEVLSD 109          
BLAST of Sh3bp2 vs. Planmine SMEST
Match: SMESG000072396.1 (SMESG000072396.1)

HSP 1 Score: 149.828 bits (377), Expect = 3.911e-41
Identity = 96/303 (31.68%), Postives = 163/303 (53.80%), Query Frame = 3
Query:   45 LPAQELLKDPNVGFSRVLKHNFSKKNYLNRWVKCFIIITKGILYVYSSTESTKPYMIVLLGIFQEIEKVKNAMESPTWVFHLHPHPELQTMPQLDFGTEVLSDVDICVNVIIEHMVISKKMYF----------SAKQAMDFRNF-----------TLTANNK----GSSQRALFQIPPEGEVT--LNSSIFGYYDFAYQNPL---NLKNIIFSGTSEAAYKELFHNFYLGSFLVRQNDDRQVLTVQSKDKVLKYVLNTNPETKLISVNKQKMEFDNLQCLLSYYQEFDLPWEKLKLTIPYKLV 863
            LPAQ LL+D +V FS  L+   +  ++   W+KC+++I+ G +Y+YSS+ S KP ++ +LG F +I+ +KN ++ P WVF L P   + ++P+L F      +++  ++     +++SK              S K  M+   +           TL  ++K          +FQI P       L  ++  + + + ++     N++ +IF GT E A+ EL    YLGS+LVRQ++ RQ+LTV+ +  ++KY L ++P+T  I +  QK  F+N+  LLSYY E  LP +  KL IP+K +
Sbjct:   10 LPAQILLQDSSVTFSGYLERKITMLSF-KHWIKCYVVISNGNIYIYSSSTSPKPVLVCILGAFHQIQIIKNRIQPPFWVFTLKPL--IDSVPELKFAAASEREMNFWISEFKLGIILSKNTQLKDDSERISSQSCKNNMEGSIYSTVSERNEIVDTLLHSDKINIYEEPDDLIFQINPVNPTAPPLYPTLTQFDNLSLKSDTSDENVEYVIFYGTREEAFSELLKRPYLGSYLVRQDNGRQILTVKCESNIVKYCLLSDPKTDRIHIAGQKESFENVYHLLSYYHEHYLPNQNCKLLIPFKFI 309          
BLAST of Sh3bp2 vs. Planmine SMEST
Match: SMESG000072391.1 (SMESG000072391.1)

HSP 1 Score: 131.339 bits (329), Expect = 2.515e-34
Identity = 87/265 (32.83%), Postives = 138/265 (52.08%), Query Frame = 3
Query:  135 WVKCFIIITKGILYVYSSTESTKPYMIVLLGIFQEIEKVKNAMESPTWVFHLHPHPELQTMPQLDFGT---EVLSDVDICVNVIIEHMVISKKMYFSAKQAMDFR------NFTLTANNKGSSQRALFQIPPE--------------GEVTLNSSIFGYYDFAYQNPLNLKNIIFSGTSEAAYKELFHNFYLGSFLVRQNDDRQVLTVQSKDKVLKYVLNTNPETKLISVNKQKMEFDNLQCLLSYYQEFDLPWEKLKLTIPYKL 860
            WVK + I+ KG  YVYS+ ++ +P M+V+L    ++E   N        F +  +    ++ QL FGT   E+LS +    N   E +      YF++ +  DF+      N      N  + +  ++ +P                 E +  +SI+   D    N +NL ++IF GTS  AY+EL  N   G++LVR+ ++ + LTVQ++D+VLKYVL TN     + +  Q+M+F++LQ LL+YY + D+P  K KL IPYKL
Sbjct:   35 WVKVYTILFKGSFYVYSNVDAKQPKMVVILTASSKVEITSNRKNRYMLSFTVFSNSNDNSIRQLKFGTYSQEILSTLMKSFN---ESINRGANNYFTSNEPNDFKMSLNRVNSNTHFENNVNEELFIYDMPERPVIGFKNGMPDFDLSETSSQNSIYLSIDSETYN-INLDDVIFKGTSYEAYQELEKNVCYGAYLVREENNAKRLTVQTRDEVLKYVLITNTNNNFVQIQNQEMKFNSLQDLLAYYHKNDIPGRKCKLVIPYKL 295          
The following BLAST results are available for this feature:
BLAST of Sh3bp2 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sh3bp2 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sh3bp2 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sh3bp2 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sh3bp2 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sh3bp2 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sh3bp2 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sh3bp2 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
S5WMZ91.245e-1040.96Sh3bp2 OS=Schmidtea mediterranea OX=79327 PE=2 SV=... [more]
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BLAST of Sh3bp2 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sh3bp2 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sh3bp2 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sh3bp2 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sh3bp2 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of Sh3bp2 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000072377.15.127e-11990.32SMESG000072377.1[more]
SMESG000072377.17.845e-11790.32SMESG000072377.1[more]
SMESG000072363.16.377e-7297.25SMESG000072363.1[more]
SMESG000072396.13.911e-4131.68SMESG000072396.1[more]
SMESG000072391.12.515e-3432.83SMESG000072391.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021695 ID=SMED30021695|Name=Sh3bp2|organism=Schmidtea mediterranea sexual|type=transcript|length=1467bp
CGGAAAAGTTATAGAAGTCACTAAAAATGACAATCGAACGAATTTTACCT
GCTCAAGAGCTTCTAAAGGATCCTAATGTTGGGTTTTCCAGAGTACTCAA
ACATAACTTTTCTAAGAAAAATTATCTCAACAGATGGGTGAAATGTTTCA
TTATAATTACAAAAGGCATTCTTTATGTCTATTCAAGTACAGAATCGACA
AAACCATACATGATTGTTTTATTGGGTATATTTCAAGAAATAGAGAAAGT
CAAGAATGCAATGGAATCTCCAACGTGGGTTTTCCATTTACATCCACACC
CAGAACTACAAACTATGCCTCAGTTAGATTTCGGAACGGAAGTATTATCA
GATGTAGACATTTGTGTAAATGTCATTATTGAACATATGGTTATTAGCAA
GAAAATGTACTTTTCAGCAAAACAAGCAATGGATTTTCGAAATTTTACGT
TGACTGCCAACAATAAAGGTTCTTCTCAAAGAGCGTTATTTCAAATTCCT
CCTGAAGGTGAGGTTACTTTAAATTCTTCCATATTCGGATATTATGATTT
CGCTTATCAAAATCCACTAAACCTCAAAAATATTATTTTCTCTGGAACAA
GTGAAGCTGCTTACAAAGAGTTATTTCATAATTTTTATCTAGGTTCATTT
CTGGTCAGACAAAATGATGATAGGCAGGTTTTGACAGTTCAAAGCAAAGA
CAAAGTTTTAAAATATGTTTTAAACACAAATCCGGAAACTAAGTTAATTT
CAGTTAACAAACAGAAGATGGAATTTGATAATTTGCAGTGCTTATTGTCG
TATTATCAAGAGTTTGACTTACCTTGGGAAAAATTGAAACTTACAATTCC
TTACAAATTGGTTGACAGAGATGAATGGCTGTGATACTGAAAAAAAAGAA
TTCTTTTTGAATTCTTTTTTTTGATTTATCATTCTATATTTCCTTTTAAT
AACCTTTAAAAACTCACTAAACTTTTATTTTCAGACTCTGATGACCCGTT
TGTTAAGCAGAGATCATGATTATAAATAAAAATGATTTCAATAAACCAGG
GGTCTCAAACTCAAAGTCTAACTCGGGCCTGGTGTGAGTAAAAGCATAAC
CCCAGGGGTCGCATTACTTAAAATTACATAACTCTGATAAGTTTGGTTAA
ATTACAAAATCCATGTGCCTCGTTTCGGGCATCTAAAGACAACGTCGTTG
GCCGCGTTTAGAGATCCTTGCGTTAGAGTAAGCTGCTGAAGGCAAACCAT
AGGATGCAGTGATGTATTAGAATTTTATAGAGATCAGTTAATAAAATAAG
TCAGTGGTCTTCAAAGTGGGTTCCATAAAAAATAGATTTTGAGTATTTTT
TAAGGCTTAATGTAACGGATTTTAAAATCAAAACTATGTTAATAAATATT
AAAAAAGAATTTTTTAAAGCCTTAGTTTGACGCTTTAGAGAGAATCCATT
AAAGACGTCCACTAAGA
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protein sequence of SMED30021695-orf-1

>SMED30021695-orf-1 ID=SMED30021695-orf-1|Name=SMED30021695-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=286bp
MTIERILPAQELLKDPNVGFSRVLKHNFSKKNYLNRWVKCFIIITKGILY
VYSSTESTKPYMIVLLGIFQEIEKVKNAMESPTWVFHLHPHPELQTMPQL
DFGTEVLSDVDICVNVIIEHMVISKKMYFSAKQAMDFRNFTLTANNKGSS
QRALFQIPPEGEVTLNSSIFGYYDFAYQNPLNLKNIIFSGTSEAAYKELF
HNFYLGSFLVRQNDDRQVLTVQSKDKVLKYVLNTNPETKLISVNKQKMEF
DNLQCLLSYYQEFDLPWEKLKLTIPYKLVDRDEWL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0005070SH3/SH2 adaptor activity
Vocabulary: biological process
TermDefinition
GO:0007165signal transduction
GO:0009967positive regulation of signal transduction
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR000980SH2
IPR011993PH-like_dom_sf
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 20..38